Keyshawn Wells rose before officials of the Chicago public school system at a meeting on the closing of his school, Mahalia Jackson elementary, and made his case. The room was silent as Keyshawn, who has impaired hearing, signed his presentation. As his two-minute time limit approached, he signed "thank you". Then GC Middleton, a teacher at the school, broke the silence, telling officials at the Monday night meeting: "If you want to know what he said, please come to Mahalia Jackson."

The crowd roared. The school has one of the only programs for the hearing impaired on the Far South Side, and teaches sign language to all students. If it closes, students will be transferred to a school over an hour's walk away.

Mahalia Jackson is one of 54 schools that the Chicago public school system (CPS) recently announced would close at the end of this year, affecting more than 30,000 students.

Elsewhere in the city, at often rowdy meetings, parents and students objected to the closures CPS officials claim are necessary to plug a $1bn deficit. CPS argues that consolidating under-used and under-performing schools will save $560m over 10 years by reducing investment in shuttered buildings. Teaching unions and community activists insist the savings have been overstated, and that the social costs of closing these schools, predominantly in low-income black and Latino neighbourhoods, far outweigh any budgetary benefit.

Monday night offered one of the last chances for the school to make its case. Almost 200 parents, students, former teachers and alum came to the meeting at Harper high school to argue to keep the school open. The officials looked on impassively, refusing to answer direct questions but to pass concerns on to the school board executive, as more than 20 people insisted that closing the school would have a devastating effect on students and the community, and made no sense, since the school they are going to be sent to is worse equipped.

Jymette Penson, the co-chair of the local school council, whose two grandchildren go to the school – as did their parents – is not so sure. Mayor Rahm Emanuel has already said the time for negotiations are over. Some activists are calling for a boycott. Penson said: "They set up these things so they can say you have free speech – and then they do what they were going to do anyway."

Mimicking the school board's response, she continued: "'Go ahead and talk. It don't mean squat to us'."

With the overwhelming number of schools being closed in black and Latino neighbourhoods, a few decried the closures as racist. "Eighty eight percent of the people who are affected by these schools closings come from minorities," said one mother. "But the decisions are being made by white people who do not have their children in these schools."

Others lambasted Chicago for its skewed priorities. "You're trying to find the money to correct the city budget problems on the backs of our children and that is unacceptable," said one.

One recurring concern was for the fate of the children in the school's autistic program. "I had one sixth-grader who couldn't speak when he came to Mahalia Jackson. Now he can say "Hi mom, hi dad," and is making great progress socially. What is going to happen to him?"

There was also a worry about children crossing gang lines to go to the receiving school, Fort Dearborn.

In many ways, Mahalia Jackson is typical of the schools in Chicago's sights. Its student body is 98% black and 75% low-income. The school's mission statement, on display in the lobby, reads: "To enable all young people, especially those who need us most, to reach their potential as productive, caring, responsible citizens."

Clearly the school is struggling to fulfil its mission. It is on its third principal in three years. According to CPS performance criteria, it is in low academic standing. Its students test far lower than the city and state average in reading, maths and science. Only 5% exceed state standards as a whole. Since 2006, its enrolment has shrunk by 22% to its lowest in eight years.

According to CPS, "ideal program enrolment" criteria, which multiplies the number of allotted classrooms by 30 – the optimum number of children in a class – the building can hold 750 students. At present it has 302. When Middleton arrived there were three seventh and eighth grade classes. Now there is only one of each and she uses twice as much space to teach a class as she once did.

"For too long, children in certain parts of Chicago have been cheated out of the resources they need to succeed, because they are in underutilized, under-resourced schools," said Barbara Byrd-Bennett, CPS's chief executive, explaining the announcement. "The district must consolidate … to get students into higher-performing schools."

Jesse Sharkey, the vice-president of the Chicago Teachers Union (CTU), says this is a non sequitur. "Parents and communities have been campaigning for more resources and better schools for years and their demands have fallen on deaf ears in city hall," he said.

"Something should be done to make sure the children at Mahalia Jackson get a better shot than they are currently getting and, on paper at least, one thing the city might do is close the school in which so many appear to be faring so poorly and send them somewhere else. But Mahalia Jackson does not exist on paper."

The school sits in the Gresham-Englewood neighbourhood, bordered on two sides by a railway track, in a zip code where more than a third of the families with children live in poverty, and well-kept homes with well-tended lawns are interspersed with boarded-up houses. A banner hanging from the front railing spells out the school's name in sign language. It has a comprehensive program for the hearing impaired. It has with special carpeting and lighting that does not buzz. The closest school with similar facilities, says Middleton, is almost 10 miles away.

Indeed, almost 20% of the children at the school have some kind of special educational needs (SEN) – a 40% higher ration than the system as a whole – ranging from autism to general behavioural difficulties. These children generally need smaller class sizes – a factor not fully taken into account in CPS's calculations. They also need more support services.

A protester is arrested in front of Chicago City Hall during a demonstration against school closures and cuts. Photograph: James Fassinger for the Guardian James Fassinger/Guardian

"The physical therapist, the case worker, the occupational therapist, the social worker, the counsellor … all have their own offices," explains Middleton. "Not all of them are here all the time, but when they are, they don't have to meet with children in a closet or the corridor like they do in other schools. I can't think of a single room in the building that isn't used."

And despite their disabilities, almost all children with special educational needs do the same tests as the non-SEN children, and their scores are included in the averages without any weighting.

"When you see the numbers, it's one thing. But when you actually see the child, it's quite different," says Katie Osgood, a teacher at a psychiatric hospital in the city. "A lot of them already come from quite chaotic home lives. The children I work with can't be in a large noisy classroom. They need space to be by themselves."

So the academic standards at Mahalia Jackson are not quite as low as they at first appear, and the school is not quite as empty as the official statistics suggest. (Not least because while calculated at 30 to a classroom, the actual CPS target is 28 to a room.) Fort Dearborn is a 13-minute walk away on the other side of the railway tracks. The area is not gang-infested but, as many mentioned at the meeting, there has been a longstanding rivalry between the two schools which has occasionally gotten out of hand. "My daughter had friends across the tracks," says Penson. "She used to fight her way over there and then fight her way back."

Since 2006, Fort Dearborn's enrolment has plummeted by 45%. According to CPS's "ideal program enrollment", its building could hold 990 students. This year 452 enrolled. With two under-enrolled schools so close together, the case for closure of one of them would seem to be sealed. But it's precisely at this point that the CPS's arguments start to fall apart.

Fort Dearborn, which is in the same zip code, seems to struggle with the same issues Mahalia Jackson does. Its student body is 98% black and 94% low-income. Its test scores are higher – in maths it is better than the city average. But it has half the percentage of SEN children. It is also on probation and in low academic standing. So there are no grounds to believe Mahalia Jackson's students would be going to a better place academically.

This, too, is typical. A study, When Schools Close, by the University of Chicago revealed that from 38 schools closed between 2001 and 2006, only 6% of students who were moved went to high-performing schools.

The financial case is also weak. Closing schools costs money, and of the scores of schools closed in the last 10 years, CPS has only been able to sell on around half. The rest require maintenance or fall into dereliction and become sites for drug dealing in run-down neighbourhoods.

"Our research found that school districts tended to save under $1m per school closed," said Emily Dowdall, a senior associate at the Pew Charitable Trusts, told the New York Times. "So in some ways that's not a game-changing amount."

Moreover, a short walk around Mahalia Jackson reveals that if too many schools is the source of the problem, the very people responsible for closure are in no small part to blame, because even as they argue for closures they keep opening new schools. Several charter schools – publicly funded, privately run and often for-profit – have opened with the blessing of CPS in the past eight years. One has an intake which overlaps with Fort Dearborn and Mahalia Jackson, and one is identical.

The one school that takes in exactly the same age range – Learn charter school – has been open for just a few years. It has a higher percentage of low-income students than Mahalia Jackson, but lower than Fort Dearborn and a lower percentage of SEN students than both. Its test scores are comparable to Fort Dearborn.

In short, the closure of Mahalia Jackson is guaranteed to cause a huge disruption to those who go there and is unlikely to save much money or improve the lot of its students. The union and community organisations have vowed to fight the closures through direct action.

Nobody is arguing that no school should ever close. But many are questioning the rationale for closing this number of schools, at this time, in this way. "We're signaling that there is going to be a large and determined movement that will use the tactics of civil disobedience and direct action in order to keep these schools open," said Jesse Sharkey, shortly after he was arrested outside City Hall two weeks ago, at a demonstration against the closures.

"We see this event as kicking off an extended campaign this spring and we think it was a great success."

On Monday night, one of the few white people in the crowd took the mic, turned her back on the board and announced she was from Occupy CPS. She called for names of people who wanted to take further direct action and then handed out leaflets for direct action training.

Some schools may go into occupation. But they admit they have an uphill struggle. "People mistakenly think if it's not their school that's going to be affected then its not going to affect them. But it's going to affect everybody," says Katie Osgood.

The fact that the closures are happening in low-income black and Latino neighbourhoods makes organising city-wide opposition difficult. "Chicago has been a deliberately segregated city for over 100 years, and this is a legacy of that and a continuation of that," says Cassie Creswell of Raise Your Hand. "I think it's going to be tough to stop them but we are obligated to try. Chicago is not a poor city; Illinois is not a poor state. The US is not a poor country. We don't have to do this."

Middleton still thinks there is room to persuade the city of its error. "But if we are going down, we're going down fighting."